A groundbreaking study that investigates how genome sequencing can be incorporated into the clinical care of children with cancer will launch at Baylor College of Medicine and Texas Children's Cancer Center with support from a $6 million grant from the National Human Genome Research Institute and the National Cancer Institute.

The Clinical Sequencing Exploratory grant from the NHGRI and NCI, which are part of the National Institutes of Health, was awarded to co-investigators Dr. Sharon Plon, a medical geneticist and professor of pediatrics – hematology/oncology at BCM, and Dr. Will Parsons, a pediatric oncologist and assistant professor of pediatrics – hematology/oncology at BCM.

Measuring use of new technology

"The questions we're asking in this study are not the typical research questions, such as whether a gene is associated with a certain disease," said Plon, who is also professor in molecular and human genetics and director of BCM's Cancer Genetics Clinic. "Rather, we're exploring how often we find things through sequencing that are important to the doctor and to the patient's family and how well doctors and parents understand the results of genetic testing. We'll be measuring how well we can use this new technology to help take care of cancer patients."

The study is comprised of three integrated projects.

Project 1 focuses on the enrollment of patients/parents in the study and assessment of the clinical impact of the genetic sequencing results.

Project 2 focuses on the generation of high-quality whole exome tumor and germline data in the CLIA-certified Whole Genome Laboratory at BCM and development of American College of Medical Genetics and CLIA compliant innovative genetic test reports for these data. The WGL is a joint effort of the BCM Medical Genetics Laboratories and Human Genome Sequencing Center, which are led by geneticists Dr. Christine Eng and Richard Gibbs.

Project 3 focuses on the ethical and social implications of the sequencing results, including analysis of the process of shared decision making between oncologists and parents as well as development of appropriate communication tools and best practices for conveying this complex genomic data to parents.

The study will be open to new patients at the Texas Children's Cancer Center with high-risk brain tumors or solid tumors. It is expected to start enrolling patients in March.

Used as guide for patient care

"Genomic sequencing technologies have become a valuable tool for research and it is presumed that they will eventually be used to guide patient care," said Parsons, who is also an assistant professor of molecular and human genetics at BCM and director of the Center for Personal Cancer Genomics and Therapeutics at TCCC. "But at this point, the process for how you would actually do that in a clinically appropriate way is still unclear. We expect to answer some important questions about the clinical application of genome sequencing through this study."

Once enrolled, blood and tumor samples from the patient will be sent to the BCM Whole Genome Laboratory, where sequencing of all the genes in the samples will be conducted. Meanwhile, the patient will start the standard treatment for his or her cancer.

"Children with cancer are put on very well-developed treatment protocols and that will continue to be the case," Parsons said.

Tumor and germline sequencing results for each patient will be available approximately three months after diagnosis and will be reported back to the parents in a meeting with the patient's oncologist and genetic counselors. The impact of these results on guiding further cancer treatment will then be evaluated, including how the data might impact decision making for patients with recurrent cancers, explained Parsons.

"The treatment options are much less clear for patients whose cancers return after initial therapy," Parsons said. "We want to learn how having genomic sequence information about the tumor would affect the decisions made by families and their oncologists about available treatments at recurrence."

In addition, a second meeting with a genetic counselor, physician and the patient's parents will review whether the results might have an impact on the inherited risk of cancer and other diseases for both the patient and other family members.

"This discussion could include things like, did we learn anything about what might have caused the child to develop cancer, was there anything in the genes that suggested the child had a genetic risk for cancer and might need screening for other types of cancer or that there might be other family members who might be at increased risk of cancer," Plon said.

Investigators will study what parents want to learn about these risks and how much these preferences vary among families.

Special ethical concerns

"When you sequence all of someone's genes, you may learn about all kinds of diseases – not just what caused the cancer but perhaps that the child is at risk for heart disease or for learning problems, something unrelated to their current medical problem," said Plon. Dr. Laurence McCullough, professor of medicine and medical ethics at BCM, will focus on the special ethical issues that occur in genome studies when the patient is a young child, including the discussion of results with parents of the potential for disease in the future.

The parent-physician meetings will be audio taped and a subset of parents will be further interviewed. The study will rely on existing strategies in analyzing physician-patient/parent communication developed at BCM under Dr. Richard Street, assistant professor of medicine – health services research.